Contacts of the strand formed by residues 220 - 226 (chain A) in PDB entry 1W75
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A PRO 5.8 0.2 + - - -
192A LYS* 3.3 34.7 + - - +
193A THR* 3.6 12.9 + - - +
194A VAL* 2.9 22.0 + - - +
219A PHE* 1.3 73.2 - - - +
221A ARG* 1.3 92.5 + - + +
315A LYS* 3.2 16.0 - - - +
317A THR* 2.8 27.1 + - - +
318A GLN* 5.3 0.8 + - - +
477A ALA 6.1 0.2 - - - +
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A THR* 4.1 10.3 - - - +
194A VAL 3.3 2.0 + - - -
195A THR* 3.2 15.7 - - - +
196A ILE 3.1 22.5 + - - -
219A PHE* 3.3 10.5 - - - -
220A ARG* 1.3 119.5 - - + +
222A ALA* 1.3 62.5 + - - +
317A THR* 3.8 7.4 - - - +
318A GLN* 2.8 46.4 + - - +
476A PHE* 3.3 14.0 + - + -
477A ALA 3.0 28.3 + - - -
478A LYS 3.1 22.2 + - - -
479A THR* 3.4 7.7 + - - +
480A GLY* 3.3 21.9 - - - +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A THR* 4.4 0.2 - - - -
196A ILE* 3.4 6.1 - - + +
206A VAL* 3.6 16.2 - - + -
210A ILE* 3.5 35.4 - - + -
219A PHE* 4.2 5.6 - - + -
221A ARG* 1.3 80.2 - - - +
223A ILE* 1.3 63.9 + - - +
224A LEU* 4.4 1.3 - - + -
317A THR* 5.4 0.7 - - + -
318A GLN 3.6 4.8 + - - +
319A ILE* 3.3 11.6 - - + +
320A LEU 3.0 22.5 + - - -
476A PHE* 3.6 3.6 - - - -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A MET* 4.2 5.6 - - + -
195A THR* 3.9 18.2 - - + -
196A ILE 3.0 6.1 + - - -
197A PHE* 3.4 28.5 - - + -
198A GLY 3.5 5.0 + - - -
206A VAL* 3.6 7.8 - - - +
222A ALA* 1.3 78.4 - - - +
224A LEU* 1.3 63.0 + - - +
225A GLN* 4.1 14.8 - - + +
320A LEU* 3.0 27.8 - - + +
473A TRP* 3.6 61.0 - - + +
476A PHE* 3.8 17.7 - - + -
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLY 4.0 3.6 - - - -
203A GLY* 3.4 23.8 - - - +
206A VAL* 3.7 15.9 - - + -
207A GLY* 3.9 13.7 - - - -
210A ILE* 4.5 8.3 - - + -
222A ALA* 4.4 9.0 - - + +
223A ILE* 1.3 83.1 - - - +
225A GLN* 1.3 62.9 + - - +
226A SER 3.9 0.4 + - - -
227A GLY 3.6 18.4 - - - +
228A SER* 4.2 7.9 - - - -
319A ILE* 4.6 8.3 - - + -
320A LEU 3.0 7.4 + - - -
321A LEU* 3.2 38.6 - - + +
322A GLY 3.3 5.2 + - - +
404A LEU* 4.4 0.9 - - + +
407A PHE* 3.8 26.7 - - + -
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Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TRP* 4.1 11.2 - - - -
197A PHE* 3.8 16.3 - - - +
198A GLY 3.1 10.5 + - - +
199A GLU* 3.1 13.5 - - + +
200A SER 2.9 26.2 + - - -
203A GLY* 4.4 0.2 - - - -
223A ILE* 4.1 7.1 - - + +
224A LEU* 1.3 73.0 - - - +
226A SER* 1.3 63.9 + - - +
227A GLY* 3.2 2.3 + - - -
421A TYR* 3.2 21.5 - - - +
443A GLU* 2.8 38.8 + - - +
444A ILE* 4.2 7.1 - - - +
447A VAL* 3.8 13.7 - - - +
473A TRP* 2.8 33.5 + - + -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 4.3 11.2 + - - -
200A SER* 3.5 15.1 + - - -
224A LEU 3.9 0.8 + - - -
225A GLN* 1.3 74.3 - - - +
227A GLY* 1.3 56.9 + - - +
233A TRP* 5.0 1.6 - - - -
322A GLY 2.8 20.8 + - - -
323A VAL* 4.1 2.0 - - - -
324A ASN* 3.9 15.8 + - - -
327A GLU* 2.7 35.1 + - - -
400A VAL* 3.5 23.1 - - - +
421A TYR* 5.1 0.5 + - - -
440A HIS* 4.2 8.0 - - - -
441A GLY 5.4 0.2 + - - -
443A GLU* 4.5 5.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il